For international flights, in my experience on private flights, you file a passenger list which includes passport numbers. But also in my experience there is never any check while boarding even in large airports, and certainly not in small airports when flying privately. And even on arrival, passport checks through GA areas seem pretty sporadic. So smuggling people would be easy.
Is it possible for there to be 'intervention' before my plane gets anywhere near an airport - in maritime situations boats often get intercepted as soon as they enter Australian waters, but is there an aviation equivalent?
It's uncommon, but certainly possible. Would probably only be done in the case of a particular suspicion. The aircraft would be visible on radar, its transponder should identify it and link it to a flight plan and alarm bells will ring if there is no match or no transponder response. I guess rather than very expensive and difficult in-the-air intercepts, a suspicious flight would find a welcoming committee waiting for it on the ground.